This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. We have recently developed a novel high capacity ion trap-quadrupole mass spectrometer, which we have described previously: A.N. Krutchinsky, H. Cohen, B.T. Chait A novel high-capacity ion trap-quadrupole tandem mass spectrometer Int J Mass Spectrom, 268 (2007) 93-105 and for which we have been granted a US patent. We have continued this development by constructing a second generation instrument as described below: A high-capacity ion trap coupled to a time-of-flight(TOF) mass spectrometer has been developed to carry out comprehensive linked scan analysis of all stored ions in the ion trap. The approach involves a novel tapered geometry high-capacity ion trap that can store more than 10^6 ions (range 800[unreadable]4000 m/z) without degrading its performance. Ions are stored and scanned out from the high-capacity ion trap as a function of m/z, collisionally fragmented and analyzed by TOF. Accurate mass analysis is achieved on both the precursor and fragments of all species ejected from the ion trap. We demonstrate the approach for comprehensive linked-scan identification of phosphopeptides in mixtures with their corresponding unphosphorylated peptides. A paper describing this work has been published: S. Myung, H. Cohen, D. Feny[unreadable], J.C. Padovan, A.N. Krutchinsky, B.T. Chait. "High-capacity ion trap coupled to a time-of-flight mass spectrometer for comprehensive linked scans with no scanning losses", International Journal of Mass Spectrometry 2010. In press